My Magento version is and had SUPEE-1533 installed.

As per Magento guidelines I have reverted this patch and then applied SUPEE-3941 (previously not applied). These step went successfully. Now when I tried to apply PATCH_SUPEE-8788_EE_1.13.1.0_v2-2016-10-14-11-52-21.sh throwing below error output -

$ ./PATCH_SUPEE-8788_EE_1.13.1.0_v2-2016-10-14-11-52-21.sh`
Checking if patch can be applied/reverted successfully...
/usr/bin/patch:  malformed patch at line 6139:
ERROR: Patch can't be applied/reverted successfully.

I have downloaded patch file directly from Magento server.

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